Grin1 (glutamate ionotropic receptor NMDA type subunit 1) - Rat Genome Database

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Gene: Grin1 (glutamate ionotropic receptor NMDA type subunit 1) Rattus norvegicus
Analyze
Symbol: Grin1
Name: glutamate ionotropic receptor NMDA type subunit 1
RGD ID: 2736
Description: Exhibits several functions, including amino acid binding activity; amyloid-beta binding activity; and ligand-gated ion channel activity. Involved in several processes, including positive regulation of cellular metabolic process; positive regulation of dendritic spine maintenance; and protein heterotetramerization. Localizes to several cellular components, including dendrite; hippocampal mossy fiber to CA3 synapse; and integral component of plasma membrane. Biomarker of cognitive disorder; middle cerebral artery infarction; placental insufficiency; sciatic neuropathy; and status epilepticus. Human ortholog(s) of this gene implicated in alcohol use disorder; autosomal dominant non-syndromic intellectual disability 8; and cerebral infarction. Orthologous to human GRIN1 (glutamate ionotropic receptor NMDA type subunit 1); PARTICIPATES IN excitatory synaptic transmission pathway; alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; (25R)-cholest-5-ene-3beta,26-diol; (R)-lipoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: GluN1; glutamate [NMDA] receptor subunit zeta-1; glutamate receptor ionotropic, NMDA 1; glutamate receptor, ionotropic, N-methyl D-aspartate 1; N-methyl-D-aspartate glutamate receptor; N-methyl-D-aspartate receptor; N-methyl-D-aspartate receptor subunit NR1; neurotransmitter receptor; NMD-R1; NMDA R1 receptor C1 cassette; NMDAR1; NR1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.0 Ensembl32,506,896 - 2,534,663 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.032,507,745 - 2,534,664 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.032,489,158 - 2,516,082 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,453,784 - 3,480,381 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.133,453,783 - 3,480,381 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(25R)-cholest-5-ene-3beta,26-diol  (EXP)
(R)-lipoic acid  (EXP)
(S)-3,5-dihydroxyphenylglycine  (EXP)
1,2-dichloroethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-methyl-6-(phenylethynyl)pyridine  (EXP)
2-methylcholine  (ISO)
26-hydroxycholesterol  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
4-[1-hydroxy-2-[4-(phenylmethyl)-1-piperidinyl]propyl]phenol  (EXP)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
agmatine  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
astaxanthin  (EXP)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
capsaicin  (EXP)
celecoxib  (ISO)
chlorpyrifos  (EXP)
choline  (EXP,ISO)
clozapine  (EXP,ISO)
cocaine  (EXP,ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
D-glucose  (ISO)
DDE  (EXP)
decabromodiphenyl ether  (EXP,ISO)
dexamethasone  (EXP)
dextromethorphan  (EXP)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (EXP,ISO)
dopamine  (EXP)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
excitatory amino acid agonist  (ISO)
felbamate  (EXP)
fenvalerate  (EXP)
folic acid  (EXP,ISO)
fucoxanthin  (ISO)
fulvestrant  (EXP)
gamma-tocopherol  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glyphosate  (ISO)
haloperidol  (EXP)
herbicide  (ISO)
homocysteine  (EXP)
kainic acid  (EXP,ISO)
ketamine  (EXP)
KT 5720  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
lead(II) chloride  (EXP)
linuron  (EXP)
lipoic acid  (EXP)
lipoteichoic acid  (ISO)
lithium chloride  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
melamine  (EXP)
methamphetamine  (EXP)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (EXP)
monosodium L-glutamate  (EXP)
morphine  (EXP,ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
nobiletin  (EXP)
Nonylphenol  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
notoginsenoside R1  (ISO)
ochratoxin A  (ISO)
oxidopamine  (EXP)
oxybenzone  (EXP)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
parathion  (EXP)
PCB138  (EXP)
pentobarbital  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phencyclidine  (ISO)
phenytoin  (EXP)
picloram  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
resveratrol  (EXP,ISO)
semicarbazide  (ISO)
SKF 38393  (EXP)
sodium arsenite  (EXP,ISO)
streptozocin  (EXP)
sulfur dioxide  (EXP)
sulindac  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
tocopherol  (ISO)
toluene  (ISO)
tributylstannane  (EXP)
trichlopyr  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (EXP)
vinclozolin  (EXP)
WIN 55212-2  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (ISO)
associative learning  (ISO)
calcium ion homeostasis  (ISO)
calcium ion transmembrane import into cytosol  (IEA,ISO)
calcium ion transport  (ISO)
calcium-mediated signaling  (IEA)
cation transport  (ISO)
cellular calcium ion homeostasis  (ISO)
cellular response to amyloid-beta  (ISO)
cellular response to manganese ion  (IEP)
cerebral cortex development  (ISO)
chemical synaptic transmission  (IBA)
conditioned taste aversion  (ISO)
excitatory postsynaptic potential  (ISO)
ionotropic glutamate receptor signaling pathway  (IBA,IDA,IEA,ISO)
learning  (ISO)
learning or memory  (ISO,TAS)
long-term memory  (ISO)
male mating behavior  (ISO)
memory  (ISO)
negative regulation of neuron apoptotic process  (ISO)
neuromuscular process  (ISO)
olfactory learning  (ISO)
pons maturation  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of calcium ion transport into cytosol  (IGI)
positive regulation of cell death  (IDA)
positive regulation of cysteine-type endopeptidase activity  (IGI)
positive regulation of dendritic spine maintenance  (IGI)
positive regulation of excitatory postsynaptic potential  (IDA)
positive regulation of reactive oxygen species biosynthetic process  (IGI)
positive regulation of Schwann cell migration  (IMP)
positive regulation of transcription by RNA polymerase II  (ISO)
prepulse inhibition  (ISO)
propylene metabolic process  (ISO)
protein heterotetramerization  (IDA)
protein localization to postsynaptic membrane  (ISO)
protein-containing complex assembly  (IDA)
regulation of axonogenesis  (ISO)
regulation of cell communication  (ISO)
regulation of dendrite morphogenesis  (ISO)
regulation of long-term neuronal synaptic plasticity  (ISO)
regulation of membrane potential  (IBA,IEA,ISO)
regulation of neuron apoptotic process  (ISO)
regulation of neuronal synaptic plasticity  (ISO)
regulation of presynaptic membrane potential  (IEA)
regulation of respiratory gaseous exchange  (ISO)
regulation of synapse assembly  (ISO)
regulation of synaptic plasticity  (ISO)
response to amine  (IEP)
response to amphetamine  (ISO)
response to calcium ion  (IEP)
response to ethanol  (IEA,ISO)
response to fungicide  (IEP)
response to glycine  (IEA,ISO)
response to morphine  (ISO)
response to organic cyclic compound  (IEP)
rhythmic process  (IDA)
sensory perception of pain  (ISO)
social behavior  (ISO)
startle response  (ISO)
suckling behavior  (ISO)
synaptic transmission, glutamatergic  (ISO)
visual learning  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
Alzheimer's disease pathway  (IEA)
amyotrophic lateral sclerosis pathway  (IEA)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
excitatory synaptic transmission pathway  (IDA)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
glutamate signaling pathway  (IEA)
heroin pharmacodynamics pathway  (ISO)
Huntington's disease pathway  (IEA)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term potentiation  (IEA)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
methadone pharmacokinetics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)

References

References - curated
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Additional References at PubMed
PMID:1352681   PMID:1374164   PMID:1377365   PMID:1385220   PMID:1386026   PMID:1388270   PMID:1532151   PMID:1834949   PMID:7524561   PMID:7531804   PMID:7679115   PMID:7684237  
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PMID:18801922   PMID:18809793   PMID:18927268   PMID:18936081   PMID:19020286   PMID:19185544   PMID:19238810   PMID:19361480   PMID:19365572   PMID:19394426   PMID:19399396   PMID:19407255  
PMID:19452450   PMID:19474322   PMID:19547699   PMID:19608740   PMID:19655413   PMID:19666081   PMID:19694907   PMID:19703901   PMID:19705939   PMID:19726645   PMID:19772634   PMID:19861419  
PMID:19923273   PMID:19934647   PMID:20008465   PMID:20016075   PMID:20056114   PMID:20064569   PMID:20146080   PMID:20414717   PMID:20427654   PMID:20448042   PMID:20463582   PMID:20623763  
PMID:20688433   PMID:20844142   PMID:20850419   PMID:20854252   PMID:20871158   PMID:20884369   PMID:20980539   PMID:21049621   PMID:21068333   PMID:21162311   PMID:21171367   PMID:21180126  
PMID:21185848   PMID:21292463   PMID:21293467   PMID:21310774   PMID:21355301   PMID:21368124   PMID:21397592   PMID:21499738   PMID:21522138   PMID:21669274   PMID:21719075   PMID:21734292  
PMID:21795692   PMID:21813695   PMID:21883149   PMID:21883211   PMID:21948527   PMID:22094385   PMID:22097734   PMID:22102472   PMID:22105219   PMID:22405206   PMID:22500715   PMID:22508518  
PMID:22512920   PMID:22546338   PMID:22652057   PMID:22681877   PMID:22743575   PMID:22762252   PMID:22871113   PMID:22891278   PMID:22952988   PMID:23110394   PMID:23164617   PMID:23381906  
PMID:23383317   PMID:23392471   PMID:23395379   PMID:23537341   PMID:23562375   PMID:23578394   PMID:23640243   PMID:23672716   PMID:23715865   PMID:23760273   PMID:23941530   PMID:23972471  
PMID:24029697   PMID:24040266   PMID:24069373   PMID:24072709   PMID:24184018   PMID:24278457   PMID:24360204   PMID:24388786   PMID:24442866   PMID:24607230   PMID:24663672   PMID:24916964  
PMID:25041985   PMID:25335889   PMID:25544544   PMID:25683482   PMID:25772108   PMID:25825749   PMID:25829490   PMID:25867330   PMID:25896221   PMID:25932647   PMID:25937004   PMID:26045554  
PMID:26071959   PMID:26133372   PMID:26220171   PMID:26370091   PMID:26490687   PMID:26725465   PMID:26875626   PMID:26919761   PMID:26930443   PMID:27089914   PMID:27094552   PMID:27160909  
PMID:27430327   PMID:27494324   PMID:27810863   PMID:27831563   PMID:28105280   PMID:28228639   PMID:28263869   PMID:28958939   PMID:29390057   PMID:29476059   PMID:29490264   PMID:29779156  
PMID:30500536   PMID:31277281   PMID:31444392   PMID:32015122   PMID:32553080   PMID:33122756   PMID:33339841  


Genomics

Comparative Map Data
Grin1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.0 Ensembl32,506,896 - 2,534,663 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.032,507,745 - 2,534,664 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.032,489,158 - 2,516,082 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,453,784 - 3,480,381 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.133,453,783 - 3,480,381 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBICelera
Cytogenetic Map3p13NCBI
GRIN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9137,139,154 - 137,168,756 (+)EnsemblGRCh38hg38GRCh38
GRCh389137,139,092 - 137,168,759 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379140,033,606 - 140,063,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,153,430 - 139,183,029 (+)NCBINCBI36hg18NCBI36
Build 349137,308,678 - 137,339,043NCBI
Celera9110,548,072 - 110,577,040 (+)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9109,493,914 - 109,523,231 (+)NCBIHuRef
CHM1_19140,182,355 - 140,211,903 (+)NCBICHM1_1
Grin1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,181,189 - 25,209,199 (-)NCBIGRCm39mm39
GRCm39 Ensembl225,181,193 - 25,209,199 (-)Ensembl
GRCm38225,291,177 - 25,319,187 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,291,181 - 25,319,187 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,146,697 - 25,174,683 (-)NCBIGRCm37mm9NCBIm37
MGSCv36225,114,256 - 25,140,988 (-)NCBImm8
Celera225,018,687 - 25,046,664 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.14NCBI
Grin1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,154,864 - 5,178,636 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,154,864 - 5,178,636 (+)NCBIChiLan1.0ChiLan1.0
GRIN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19137,168,543 - 137,198,297 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,168,722 - 137,197,382 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09108,198,350 - 108,228,887 (+)NCBIMhudiblu_PPA_v0panPan3
GRIN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,492,967 - 48,513,981 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,493,287 - 48,509,050 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,683,789 - 47,707,011 (-)NCBI
ROS_Cfam_1.0949,357,798 - 49,382,176 (-)NCBI
UMICH_Zoey_3.1948,135,045 - 48,158,254 (-)NCBI
UNSW_CanFamBas_1.0948,433,856 - 48,457,059 (-)NCBI
UU_Cfam_GSD_1.0948,481,015 - 48,504,246 (-)NCBI
Grin1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,536,077 - 202,560,723 (+)NCBI
SpeTri2.0NW_004936669814,330 - 838,881 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIN1
(Sus scrofa - pig)
No map positions available.
GRIN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,020,556 - 1,050,568 (-)NCBI
ChlSab1.1 Ensembl121,019,263 - 1,050,231 (-)Ensembl
Grin1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624760777,208 - 800,525 (-)NCBI

Position Markers
UniSTS:465388  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,110,316 - 8,110,962 (+)MAPPER
Rnor_6.032,514,382 - 2,515,027NCBIRnor6.0
Rnor_5.032,495,795 - 2,496,440UniSTSRnor5.0
RGSC_v3.433,460,413 - 3,461,058UniSTSRGSC3.4
Celera32,936,859 - 2,937,504UniSTS
Cytogenetic Map3p13UniSTS
PMC57740P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,108,466 - 8,108,969 (+)MAPPER
Rnor_6.032,512,532 - 2,513,034NCBIRnor6.0
Rnor_5.032,493,945 - 2,494,447UniSTSRnor5.0
RGSC_v3.433,458,563 - 3,459,065UniSTSRGSC3.4
Celera32,935,009 - 2,935,511UniSTS
Cytogenetic Map3p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:860
Count of miRNA genes:210
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000037725, ENSRNOT00000044246, ENSRNOT00000049297
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 56
Low 3 7 10 10
Below cutoff 4 10 3 6 3 4 4 6 13 21 11 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001287423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY090615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM039130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L08228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S39221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U11418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X63255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X65227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000037725   ⟹   ENSRNOP00000029227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,506,896 - 2,534,375 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000044246   ⟹   ENSRNOP00000043301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,507,745 - 2,534,663 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000049297   ⟹   ENSRNOP00000049198
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,507,745 - 2,534,663 (-)Ensembl
RefSeq Acc Id: NM_001270602   ⟹   NP_001257531
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270603   ⟹   NP_001257532
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270605   ⟹   NP_001257534
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270606   ⟹   NP_001257535
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270608   ⟹   NP_001257537
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270610   ⟹   NP_001257539
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001287423   ⟹   NP_001274352
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: NM_017010   ⟹   NP_058706
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,103,680 - 8,130,603 (-)NCBI
Rnor_6.032,507,745 - 2,534,663 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
RGSC_v3.433,453,784 - 3,480,381 (-)RGD
Celera32,930,222 - 2,957,142 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233555   ⟹   XP_006233617
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,509,012 - 2,534,664 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233556   ⟹   XP_006233618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,509,012 - 2,534,664 (-)NCBI
Rnor_5.032,489,158 - 2,516,082 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001257531 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257532 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257534 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257535 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257537 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257539 (Get FASTA)   NCBI Sequence Viewer  
  NP_001274352 (Get FASTA)   NCBI Sequence Viewer  
  NP_058706 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA19659 (Get FASTA)   NCBI Sequence Viewer  
  AAB22435 (Get FASTA)   NCBI Sequence Viewer  
  AAB50926 (Get FASTA)   NCBI Sequence Viewer  
  AAB50927 (Get FASTA)   NCBI Sequence Viewer  
  AAB50928 (Get FASTA)   NCBI Sequence Viewer  
  AAB50929 (Get FASTA)   NCBI Sequence Viewer  
  AAB50930 (Get FASTA)   NCBI Sequence Viewer  
  AAB50931 (Get FASTA)   NCBI Sequence Viewer  
  AAB50932 (Get FASTA)   NCBI Sequence Viewer  
  AAB50933 (Get FASTA)   NCBI Sequence Viewer  
  AAM09025 (Get FASTA)   NCBI Sequence Viewer  
  CAA44914 (Get FASTA)   NCBI Sequence Viewer  
  CAA46335 (Get FASTA)   NCBI Sequence Viewer  
  EDL93606 (Get FASTA)   NCBI Sequence Viewer  
  EDL93607 (Get FASTA)   NCBI Sequence Viewer  
  EDL93608 (Get FASTA)   NCBI Sequence Viewer  
  EDL93609 (Get FASTA)   NCBI Sequence Viewer  
  EDL93610 (Get FASTA)   NCBI Sequence Viewer  
  EDL93611 (Get FASTA)   NCBI Sequence Viewer  
  EDL93612 (Get FASTA)   NCBI Sequence Viewer  
  EDL93613 (Get FASTA)   NCBI Sequence Viewer  
  P35439 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058706   ⟸   NM_017010
- Peptide Label: isoform 1a precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257539   ⟸   NM_001270610
- Peptide Label: isoform 4a precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257534   ⟸   NM_001270605
- Peptide Label: isoform 2a precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257537   ⟸   NM_001270608
- Peptide Label: isoform 4b precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257532   ⟸   NM_001270603
- Peptide Label: isoform 2b precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257535   ⟸   NM_001270606
- Peptide Label: isoform 3b precursor
- UniProtKB: Q62648 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257531   ⟸   NM_001270602
- Peptide Label: isoform 1b precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233618   ⟸   XM_006233556
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006233617   ⟸   XM_006233555
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001274352   ⟸   NM_001287423
- Peptide Label: isoform 3a precursor
- UniProtKB: P35439 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000043301   ⟸   ENSRNOT00000044246
RefSeq Acc Id: ENSRNOP00000049198   ⟸   ENSRNOT00000049297
RefSeq Acc Id: ENSRNOP00000029227   ⟸   ENSRNOT00000037725
Protein Domains
Lig_chan-Glu_bd   PBPe

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691870
Promoter ID:EPDNEW_R2395
Type:initiation region
Name:Grin1_1
Description:glutamate ionotropic receptor NMDA type subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,534,579 - 2,534,639EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2736 AgrOrtholog
Ensembl Genes ENSRNOG00000011726 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000029227 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000043301 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000049198 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000037725 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000044246 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000049297 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro ANF_lig-bd_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CaM-bd_C0_NMDA_rcpt_NR1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glu/Gly-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iono_rcpt_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iontro_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripla_BP_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24408 UniProtKB/Swiss-Prot
NCBI Gene 24408 ENTREZGENE
Pfam ANF_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CaM_bdg_C0 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Grin1 PhenoGen
PRINTS NMDARECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PBPe UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53822 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NMDZ1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q62648 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q62646 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Grin1  glutamate ionotropic receptor NMDA type subunit 1  Grin1  glutamate receptor, ionotropic, N-methyl D-aspartate 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Grin1  glutamate receptor, ionotropic, N-methyl D-aspartate 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed abundantly in hypothalamus in females of all ages and present in majority of gonadotrophin releasing hormone (GnRH) neurons 625682
gene_function N-methyl-D-aspartate (NMDA) class, glutamate receptor subunit 69667
gene_function N-methyl-D-aspartate (NMDA) class, glutamate receptor subunit 628428
gene_process functions in long term potentiation, synaptic plasticity, and Ca++ influx in postsynaptic nerve cells 69667
gene_process functions in long term potentiation, synaptic plasticity, and Ca++ influx in postsynaptic nerve cells 628428
gene_process has a role in memory and learning 69667
gene_process has a role in memory and learning 628428
gene_process modulates spatial memory, synapse formation and transmission  
gene_process may play an important role in the neuronal stimulation assosicated with female reproductive physiology 625682
gene_process receptor for glutamate that influences reproductive physiology in female rats 625682
gene_process glutamatergic signaling via the receptors directly activates LH-releasing hormone (LHRH) neurons in medial nuclei of the preoptic area 625682
gene_regulation phosphorylated by different kinases such as PKC, Fyn and cdk5 69667
gene_regulation increased expression in the hippocampus occurs in response to thyroid hormone 727495
gene_regulation steroids have no effect on the mRNA levels in LH-releasing hormone (LHRH) neurons or the percentage of LHRH neurons expressing the gene 625682